Yes, that message is correct:

$ perl -Mwarnings -Mdiagnostics -e '@array = (1,2,3); print defined(@a
+rray)'
defined(@array) is deprecated at -e line 1 (#1)
    (D deprecated) defined() is not usually useful on arrays because i
+t
    checks for an undefined scalar value.  If you want to see if the
    array is empty, just use if (@array) { # not empty } for example.
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Your code:

my $tSida = $sida + 1;
if ((@annots) || (defined @{$links{'-1'}}) || (defined @{$links{$tSida
+}})) { $sidObjekt .='/Annots ' . mergeLinks() . ' 0 R';
}
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Would be better written as...

my $tSida = $sida + 1;
if( @annots || @{$links{'-1'}} || @{$links{$tSida}} ) {
  $sidObjekt .= '/Annots ' . mergLinks() . ' 0 R';
}
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Your use of defined is presumably to determine if the array ref stored in $links{'-1'} contains values. If instead you want to determine if $links{'-1'} exists, use exists. If you want to see if $links{'-1'} is defined, use defined without dereferencing the element. And if you want to see if it contains an anonymous array, you can use ref or Scalar::Util::reftype()